Figure 1
Figure 1. CDKN2A (p16ink4a) mRNA expression in human samples. (A) Study of CDKN2A mRNA expression using microarrays (U133A, 209644_x_at probe set; Affymetrix Technology, Santa Clara, CA). Evaluation was done as described14 on the 84 T-ALL samples (including Jurkat cell line) in which the status of the CDKN2A locus has been studied by Southern-blotting experiments, BAC array CGH, or oligonucleotide array CGH. D indicates that at least 1 of the CDKN2A alleles has been deleted. Expression is expressed in arbitrary units and classified according to the distribution of the noise (see “Patients, materials, and methods, Human samples and analyses” for details). P values less than .025 were considered as significant (alpha risk). NS indicates no significant expression (blue); Int, intermediate expression significant but P values greater than .01 (orange); high, high expression (P < .01; red). Cases were grouped according to oncogenic groups previously defined.14 T-ALL cases expressing significant levels of CDKN2A mRNA are identified by their unique patient number and printed with the color code defined by the level of CDKN2A expression. The order of the labels is identical to that shown in histograms. No significant expression was detected in thymocyte subsets (not shown). (B) Study of CDKN2A locus deletion by oligonucleotide aCGH. Two representative cases (TL04 and TL31) with CDKN2A locus biallelic deletions are shown. Values (−1) and (−2) represent ratio corresponding to the deletion of 1 allele and 2 alleles, respectively. TL04 shows a short deletion on both alleles, whereas TL31 shows a short deletion of 1 allele and a large 9p deletion (encompassing the second CDKN2A allele). (C) Study of CDKN2A mRNA expression by RQ-PCR and comparison with microarray data. Color code is identical to that used in panel A. RQ-PCR was performed using standard procedures. Efficiency and specificity of the p16INK4A RQ-PCR system was assessed on Hela DNA (50 ng/μL) serially diluted from 10−1 to 10−5. Calibration curves were performed using 10-fold serial dilutions of diagnostic DNA. ABL gene was used to normalize the samples. No template controls (H2O) as well as nonamplification controls (Jurkat leukemia cell-line DNA) were included in each assay. Expression lower than 10−2 was considered as not significant (ns) and not detailed in the figure.

CDKN2A (p16ink4a) mRNA expression in human samples. (A) Study of CDKN2A mRNA expression using microarrays (U133A, 209644_x_at probe set; Affymetrix Technology, Santa Clara, CA). Evaluation was done as described14  on the 84 T-ALL samples (including Jurkat cell line) in which the status of the CDKN2A locus has been studied by Southern-blotting experiments, BAC array CGH, or oligonucleotide array CGH. D indicates that at least 1 of the CDKN2A alleles has been deleted. Expression is expressed in arbitrary units and classified according to the distribution of the noise (see “Patients, materials, and methods, Human samples and analyses” for details). P values less than .025 were considered as significant (alpha risk). NS indicates no significant expression (blue); Int, intermediate expression significant but P values greater than .01 (orange); high, high expression (P < .01; red). Cases were grouped according to oncogenic groups previously defined.14  T-ALL cases expressing significant levels of CDKN2A mRNA are identified by their unique patient number and printed with the color code defined by the level of CDKN2A expression. The order of the labels is identical to that shown in histograms. No significant expression was detected in thymocyte subsets (not shown). (B) Study of CDKN2A locus deletion by oligonucleotide aCGH. Two representative cases (TL04 and TL31) with CDKN2A locus biallelic deletions are shown. Values (−1) and (−2) represent ratio corresponding to the deletion of 1 allele and 2 alleles, respectively. TL04 shows a short deletion on both alleles, whereas TL31 shows a short deletion of 1 allele and a large 9p deletion (encompassing the second CDKN2A allele). (C) Study of CDKN2A mRNA expression by RQ-PCR and comparison with microarray data. Color code is identical to that used in panel A. RQ-PCR was performed using standard procedures. Efficiency and specificity of the p16INK4A RQ-PCR system was assessed on Hela DNA (50 ng/μL) serially diluted from 10−1 to 10−5. Calibration curves were performed using 10-fold serial dilutions of diagnostic DNA. ABL gene was used to normalize the samples. No template controls (H2O) as well as nonamplification controls (Jurkat leukemia cell-line DNA) were included in each assay. Expression lower than 10−2 was considered as not significant (ns) and not detailed in the figure.

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